Origin IGS: taatttgttgaaggattgatccgaactccggttctcatgatcgatccttttattttatacgtgaattaaccaagaaattaaatagatgaattaatataacagtt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aactgttatattaattcatctatttaatttcttggttaattcacgtataaaataaaaggatcgatcatgagaaccggagttcggatcaatccttcaacaaatta Mask Tandem Repeat Region ================================================ taatttgttgaaggattgatccgaactccggttctcatgatcgatccttttattttatacgtgaattaaccaagaaattaaatagatgaattaatataacagtt Find is-nt database================================================ Query_seq: TF0082:TF0083|TF0082:TF0083:transcriptional regulator, TetR family:outer membrane efflux protein:->->:89325..89428 104 taatttgttgaaggattgatccgaactccggttctcatgatcgatccttttattttatacgtgaattaaccaagaaattaaatagatgaattaatataacagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0082:TF0083|TF0082:TF0083:transcriptional regulator, TetR family:outer membrane efflux protein:->->:89325..89428 104 taatttgttgaaggattgatccgaactccggttctcatgatcgatccttttattttatacgtgaattaaccaagaaattaaatagatgaattaatataacagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0082:TF0083|TF0082:TF0083:transcriptional regulator, TetR family:outer membrane efflux protein:->->:89325..89428 104 taatttgttgaaggattgatccgaactccggttctcatgatcgatccttttattttatacgtgaattaaccaagaaattaaatagatgaattaatataacagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatttgttgaaggattgatccgaactccggttctcatgatcgatccttttattttatacgtgaattaaccaagaaattaaatagatgaattaatataacagtt Predict ORF larger than 30AA ================================================ taatttgttgaaggattgatccgaactccggttctcatgatcgatccttttattttatacgtgaattaaccaagaaattaaatagatgaattaatataacagtt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taatttgttgaaggattgatccgaactccggttctcatgatcgatccttttattttatacgtgaattaaccaagaaattaaatagatgaattaatataacagtt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0082:TF0083|TF0082:TF0083:transcriptional regulator, TetR family:outer membrane efflux protein:->->:89325..89428 104 taatttgttgaaggattgatccgaactccggttctcatgatcgatccttttattttatacgtgaattaaccaagaaattaaatagatgaattaatataacagtt Intra-Species Hit: Count: 1 Min: 1 Max: 104 Len: 104 Subject: tfor_TF0082_TF0083|transcriptional regulator, TetR family:outer membrane efflux protein|POSITIVE:POSITIVE|[89325,89428]|104 HSP 1 e-value: 1.0E-52 bit: 206.0 Len: 104 Query Start:1 Query End:104 Subject Strand: POSITIVE Subject Start: 1 Subject End: 104 taatttgttgaaggattgatccgaactccggttctcatgatcgatccttttattttatacgtgaattaaccaagaaattaaatagatgaattaatataacagtt taatttgttgaaggattgatccgaactccggttctcatgatcgatccttttattttatacgtgaattaaccaagaaattaaatagatgaattaatataacagtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUUGUUGAAGGAUUGAUCCGAACUCCGGUUCUCAUGAUCGAUCCUUUUAUUUUAUACGUGAAUUAACCAAGAAAUUAAAUAGAUGAAUUAAUAUAACAGUU (((((..((((((((((((((.((((....))))....))))))))))))..........((......))..............))..)))))........... (-20.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACUGUUAUAUUAAUUCAUCUAUUUAAUUUCUUGGUUAAUUCACGUAUAAAAUAAAAGGAUCGAUCAUGAGAACCGGAGUUCGGAUCAAUCCUUCAACAAAUUA ...((((................((((((....))))))................((((((.((((....((((....)))).)))).)))))).))))..... (-16.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 314 65 21 217 175 tfor:TF0238|5end_outer_membrane_protein_266871..267101_POSITIVE 307 48 7 58 22 tfor:TF1586|5end_hypothetical_protein_1690971..1691201_POSITIVE 299 50 3 122 69 tfor:TF0906|5end_conserved_hypothetical_protein_949675..949905_POSITIVE 295 50 4 86 32 tfor:TF1450|5end_periplasmic_serine_protease_1534102..1534332_POSITIVE 293 54 15 90 56 tfor:TF0231|5end_conserved_hypothetical_protein_257804..258034_POSITIVE 285 50 4 183 137 tfor:TF0112|5end_outer_membrane_protein_121244..121474_POSITIVE 281 49 4 170 121 tfor:TF0992|5end_hypothetical_protein_1048251..1048481_POSITIVE 281 47 5 185 136 tfor:TF0594|5end_conserved_hypothetical_protein;_possible_PAP2_superfamily_protein_626971..627201_POSITIVE 276 48 6 90 51 tfor:TF0070|5end_possible_regulatory_element_76942..77172_POSITIVE 274 47 15 60 24 tfor:TF3026|5end_conserved_hypothetical_protein_3249137..3249367_POSITIVE 266 59 19 92 47 tfor:TF2042|5end_sugar_phosphate_isomerase,_polysialic_acid_capsule_expression_protein_2201647..2201877_POSITIVE 265 47 13 141 114 tfor:TF1243|5end_periplasmic_protease_1327243..1327473_POSITIVE 265 48 4 186 132 tfor:TF1192|5end_alpha-amylase_1274007..1274237_POSITIVE 260 49 4 220 170 tfor:TF1430|5end_hypothetical_protein_1514867..1515097_POSITIVE 260 47 6 215 178 tfor:TF0045|5end_outer_membrane_protein,_TonB_dependent_receptor_49626..49856_POSITIVE 259 63 26 182 144 tfor:TF1035|5end_iron(III)_ABC_transporter,_periplasmic-binding_protein_1095910..1096140_POSITIVE 258 47 3 146 110 tfor:TF3126|5end_glycosyltransferase,_group_2_family_3360439..3360669_POSITIVE 258 46 4 74 19 tfor:TF2766|5end_shikimate_kinase_2951619..2951849_POSITIVE 258 47 4 155 106 tfor:TF1114|5end_hypothetical_protein_1185053..1185283_POSITIVE 258 75 34 191 157 tfor:TF0495|5end_conserved_hypothetical_protein;_possible_S-layer_related_protein_precursor_520862..521092_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 314 49 11 80 42 tfor:TF0082|3end_transcriptional_regulator,_TetR_family_89264..89414_POSITIVE 293 54 15 68 34 tfor:TF0230|3end_hydrolase,_haloacid_dehalogenase-like_family_257862..258012_POSITIVE 265 48 4 78 24 tfor:TF1191|3end_possible_transcriptional_regulator_1273979..1274129_POSITIVE 259 63 26 93 55 tfor:TF1034|3end_conserved_hypothetical_protein_1095901..1096051_POSITIVE 258 47 3 138 102 tfor:TF3125|3end_recombination/repair_protein_3360511..3360661_POSITIVE 255 63 22 148 108 tfor:TF0494|3end_conserved_hypothetical_protein_520906..521056_POSITIVE 254 47 4 115 65 tfor:TF2654|3end_arginyl-tRNA_synthetase_2824559..2824709_POSITIVE 253 47 20 128 103 tfor:TF1274|3end_hypothetical_protein_1357895..1358045_POSITIVE 252 56 12 86 43 tfor:TF1328|3end_possible_cytidylyltransferase_1408650..1408800_POSITIVE 249 43 19 124 98 tfor:TF0660|3end_conserved_hypothetical_protein_707399..707549_POSITIVE 248 55 12 93 29 tfor:TF1897|3end_conserved_hypothetical_protein;_possible_aminopeptidase_2052107..2052257_POSITIVE 245 63 21 102 61 tfor:TF0533|3end_hypothetical_protein_559519..559669_POSITIVE 243 48 3 149 90 tfor:TF2020|3end_muconate_cycloisomerase_2177552..2177702_POSITIVE 242 63 21 99 62 tfor:TF1249|3end_phosphoglycerate_kinase_(cytosolic_phosphoglycerate_kinase)_1332356..1332506_POSITIVE 242 47 2 51 6 tfor:TF0490|3end_conserved_hypothetical_protein_513904..514054_POSITIVE 240 43 3 123 72 tfor:TF1160|3end_MutT/nudix_family_protein_1241008..1241158_POSITIVE 237 42 2 98 58 tfor:TF2256|3end_transfer_region-related_protein,_TraI_2428614..2428764_POSITIVE 237 44 4 149 107 tfor:TF2132|3end_TIM-barrel_protein,_NifR3_family_2308769..2308919_POSITIVE 237 47 10 145 101 tfor:TF2081|3end_phosphopantetheine_adenylyltransferase_2249031..2249181_POSITIVE 234 69 31 111 68 tfor:TF2785|3end_RNA_polymerase_sigma_factor,_ECF_subfamily_(sigma-70)_2969917..2970067_POSITIVE